Title

ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

Authors

Affiliation

¹Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India

Email

akbanerjee@biotech.buruniv.ac.in;   *Corresponding author

Article Type

software

Date

Received August 05, 2015; Accepted August 17, 2015; Published August 31, 2015

Component (bridge: ΔΔG_brd, background: ΔΔG_prot, desolvation: ΔΔG_dsolv) and net (ΔΔG_net) energy-terms of salt-bridge-structure (SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS) method. While the procedure reports gross energy terms (Kcal Mol^-1), report on bond-multiplicity corrected normalized energy-terms (Kcal Mol^-1 Bond^-1) along with their accessibility (ASA) in monomer, isolated-SBS (ISBS) and networked-SBS (NSBS) format would be very useful for statistical comparison among SBSs and understanding their location in protein structure. In this end, ADSBET2 potentially incorporates these features along with additional model for side-chain. Gross and normalized energy-terms are redirected in monomer, ISBS and NSBS format along with their ASA informations.  It works on any number of SBSs for any number of structure files present in a database. Taken together, ADSBET2 has been suitable for statistical analyses of SBSs energetics and finds applications in protein engineering and structural bioinformatics.

ADSBET2 is freely available at http://sourceforge.net/projects/ADSBET2/ for all users.

Energy terms, Networked, Isolated, Salt Bridge, ASA, Kcal Mol^-1Bond^-1

Citation

Nayek et al. Bioinformation 11(8): 413-415 (2015)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.